diff --git a/README.md b/README.md index 399f0daaf0c11acdb1bd1d553a8290d238ac53f1..a4b6f56c897d31aba5740c05c919b00f07979e86 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ To run a set of replicates from study RID: ------------------------------------------ Run in repo root dir: * `sh workflow/scripts/splitStudy.sh [studyRID]` -It will run in parallel in batches of 25 replicatesRID with 10 second delays between launches. +It will run in parallel in batches of 25 replicatesRID with 30 second delays between launches. @@ -115,4 +115,4 @@ Please cite in publications: Pipeline was developed by BICF from funding provide Pipeline Directed Acyclic Graph ------------------------------- - + \ No newline at end of file diff --git a/workflow/scripts/splitStudy.sh b/workflow/scripts/splitStudy.sh index be4259c2225b72e1e789b8c01a184930b5b86819..bade44bbdf1c06b0771bf9f0d040d660fa77fe4d 100644 --- a/workflow/scripts/splitStudy.sh +++ b/workflow/scripts/splitStudy.sh @@ -10,7 +10,7 @@ python3 ./workflow/scripts/splitStudy.py -s $1 # run pipeline on replicate RIDs in parallel module load nextflow/20.01.0 module load singularity/3.5.3 -while read repRID; do echo ${repRID}; sleep 10; done < "$1_studyRID.csv" | xargs -P 25 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} +while read repRID; do echo ${repRID}; sleep 30; done < "$1_studyRID.csv" | xargs -P 25 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} # cleanup study RID files rm $1_studyRID.json